title: R416SCAbx

city: Winston-Salem

first: Drew

last: Kiraly

state: NC

address: 115 South Chestnut Street

department: Physiology, Pharmacology, Psychiatry

institute: Wake Forest University School of Medicine

data_processing:
FastQC v0.11.6
Trimmed and filtered adaptor sequences
STAR v2.4.0
Aligned raw FASTQ files (STAR v2.4.0) to rat reference genome (Rnor_6.0) to generate transcript counts for each sample.
BioJupies/Limma package (Maayan Lab, Mt. Sinai School of Medicine)
Assembly: Raw count matricies for each sample were normalized and put into a single count file containing all samples
Supplementary files format and content: .csv
Supplementary files format and content: count matrix

source_name: Rat, Nucleus Accumbens, antibiotics (microbiome depletion) + short-chain fatty acids

growth_protocol: Male Sprague-Dawley rats (7–9 weeks old, Envigo) were group-housed (2 rats/cage) in a humidity and temperature-controlled colony room on a 24 h light–dark cycle. Drink solutions (H2O, Antibiotics, SCFA, etc.) and food were available ad libitum throughout the entirety of all experiments.

extract_protocol:
Total RNA was extracted using an Rneasy mini plus kit (Qiagen) according to manufacturer's protocol
Clontech SMARTer cDNA kit (Clontech Laboratories, Inc., Mountain View, CA USA, catalog# 634925)

tag: tissue

value: Brain

value: Sprague-Dawley (WT)

value: antibiotics + short-chain fatty acid


title: B1_AGY1614_Gen10_RepA

status: Public on May 01 2024

type: SRA

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

country: USA

institute: University of Wisconsin

description:
GaschNuSeq_1008
Batch1_Dutcher_barcode_cts.csv

library_source: other

data_processing:
library strategy: BAR-seq
Read counts generated using a script to identify samples from fastq files that are associated with each 10bp index tag
Assembly: YPS1009
Supplementary files format and content: Raw Count data, csv files

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Strains used in the study are all haploids of the YPS1009 background. 1 mL frozen glycerol stocks of librarytransformed cells were thawed into 100 mL of liquid SC-His with nourseothrycin (NTC, 100 mg/L) to ensure maintenance of amplified chromosomes and G418 (200 mg/L) to maintain plasmids at a starting OD600of 0.05, then grown in shake flasks at 30°C with shaking. The remaining cells from the frozen stocks were pelleted by centrifugation and represented the starting pool (generation 0) for each strain. After five generations, each pooled culture was diluted to an OD600of 0.05 in fresh media, in order to maintain cells in log phase. At 10 generations (and 5 generations for a subset of strains), cells were harvested and cell pellets were stored at −80°C.

extract_protocol:
Plasmids were recovered from each pool using Zymoprep Yeast Plasmid Miniprep II (Zymo Research D2004-A) with the following modifications: samples were incubated with 15 units zymolyase at 37°C for 1 hour, with inversion every 15 minutes; incubation in cell lysis buffer was extended to 10 minutes; after neutralization, samples were put on ice for 30 minutes, then centrifuged at 4°C.
Plasmid barcodes were amplified using primers containing Illumina multiplex adaptors as described in (Piotrowski et al. 2015), with number of PCR cycles reduced to 20. Barcode amplicons were pooled and purified using AxyPrep Mag beads (1.8X volume beads per sample volume) according to the manufacturer’s instructions (Axygen).

tag: strain

tag: genetic lineage

value: North American

tag: generation

tag: media

tag: molecule type

value: plasmid DNA


title: M2c_P_16C5_D3

city: South San Francisco

first: Joshua

last: Lichtman

state: CA

address: 333 Oyster Point Boulevard

department: Translational Science

institute: NGM Biopharmaceuticals

library_source: transcriptomic

data_processing:
Data raw reads were filtered using Trim Galore! to remove low quality and adaptor bases. Reads shorter than 20nt were discarded.
Filtered reads were mapped to UCSC hg19 genome sequences using STAR (v2.6.0a).
At last, counts of all samples were generated using featureCounts (v1.6.2), and edgeR (v3.22.3) was used to get normalized counts and perform differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression raw read counts in tabular data format

molecule: total RNA

organism: Homo sapiens

source_name: M2c macs, PBS and 16C5 antibody treatment

extract_protocol:
Cells were harvested in TRIzol and RNA was isolated by choroform extraction, follwed by purification with the Rneasy kit (Qiagen).
Total RNA was prepared for sequencing using the TailorMix Directional RNA Sample Preparation Kit (SeqMatic) and sequenced on an Illumina NovaSeq S1.

treatment_protocol: Peripheral blood monocytes from healthy human donors were plated on wells pre-coated with PBS or fibronectin (5 ug/mL) in the presence of an anti-KLH control antibody or anti-ILT3 16C5 (10 ug/mL). Monocytes were differentiated into dendritic cells or macrophages as follows: Monocyte-derived DCs (GM-CSF/IL-4 for 7 days), tolerogenic DCs (GM-CSF/IL-4 for 5 days + vitamin D3/dexamethasone for 2 days), or macrophages (M-CSF for 5 days plus IFN-g/LPS for 2 days for M1 macrophages, IL-4 for 2 days for M2a macrophages, or IL-10 for 2 days for M2c macrophages).

tag: cell type

value: M2c macrophage

tag: plate coating

value: PBS

tag: donor

value: Donor 3

tag: antibody treatment

value: anti-ILT3 16C5


title: HK_Male_4

city: Bellinzona

first: Marco

last: Bolis

address: Via Francesco Chiesa

country: Switzerland

institute: IOR Institute of Oncology Research

data_processing:
The overall quality of sequencing reads was evaluated using FastQC. Alignments to the reference mouse genome (GRCm38.p6) were performed using STAR (v.2.6.1c) in two-pass mode. Gene expression was quantified at the gene level by using the comprehensive annotations made available by Gencode (M25). Samples were adjusted for library size and normalized with the variance stabilizing transformation in the R statistical environment using DESeq2 (v1.28.1).
Assembly: GRCm38.p6
Supplementary files format and content: tab delimited raw count matrix, quantified at the gene level by using Gencode (M25 GTF-File) and STAR (v.2.6.1c)

organism: Mus musculus

source_name: Gastrocnemius Muscle

extract_protocol:
RNA was isolated with TRIzol reagent (Sigma-Aldrich) and purified using the Direct-zol RNA MiniPrep Kit (Zymo Research) according to the manufacturer's protocol.
RNA integrity was checked with Agilent 2100 Bioanalyzer system. Protocol used was NEBNext rRNA depletion KIT. Sequencing of the libraries was performed using the NextSeq 500 with the NextSeq 500/550 High Output Kit v2 (75 cycles; Illumina).

treatment_protocol: Haenkenium extract was administered at the dosage of 0.5 mg/kg/day in drinking water. Mice treatment started at 20 months of age. HK extract was replaced and prepared fresh on a weekly basis.

value: Gastrocnemius Muscle

tag: Sex

value: Male

tag: treatment

value: Haenkenium extract

tag: treatment dose

tag: experimental batch


title: R414SCAbx

molecule: polyA RNA

organism: Rattus norvegicus


title: HK_Male_1

value: Haenkenium extract was administered at the dosage of 0.5 mg/kg/day in drinking water


title: M2a_P_16C5_D3

source_name: M2a macs, PBS and 16C5 antibody treatment

value: M2a macrophage


title: CTRL_Female_5

value: Female

value: untreated

value: drinking water


title: CTRL_Female_1


title: O.T, snRNA-seq

city: Nantong

first: Yinchuan

last: Li

state: Jiangsu

address: 16 wenfeng road, Chongchuan

department: Medical School

country: China

institute: Nantong University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger V3.1.0. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger )
Assembly: Ensembl_release104
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: hypothalamus

extract_protocol:
Intact hypothalami were cryopreserved in liquid nitrogen from sacrificed rats and approximately 2-3 pooled intact hypothalami in each group were homogenized in 500µL ice-cold homogenization buffer (0.25 M sucrose, 5 mM CaCl2 , 3 mM MgAc2, 10 mM Tris-HCl pH 8.0, 1 mM DTT, 0.1 mM EDTA, 1x protease inhibitor, and 1 U µL−1 RiboLock RNase inhibitor) with Dounce homogenizer. Then the homogenizer was washed with 700µL ice-cold nuclei washing buffer (0.04% bovine serum albumin, 0.2 U/µL RiboLock RNase Inhibitor, 500 mM mannitol, 0.1 mM phenylmethanesulfonyl fluoride Protease Inhibitor in 1 x PBS). Next, the homogenates were filtered through a 70 µm cell strainer to collect the nuclear fraction. The nuclear fraction was mixed with an equal volume of 50% iodixanol and added on top of a 30% and 33% iodixanol gradient. This solution was then centrifuged for 20 min at 10 000 ×g at 4 °C. After the myelin layer was removed from the top of the gradient, the nuclei were collected from the 30% and 33% iodixanol interface. The nuclei were resuspended in nuclear wash buffer and resuspension buffer and pelleted for 5 min at 500 ×g at 4 °C. The nuclei were filtered through a 40 µm cell strainer to remove cell debris and large clumps and the nuclear concentration was manually assessed using trypan blue counterstaining and a hemocytometer. Finally, the nuclei were adjusted to 700–1200 nuclei µL−1, and examined with a 10X Chromium platform.
Reverse transcription, cDNA amplification and library preparation were performed based on the protocol from 10X Genomics. Briefly, nuclei were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 5’ Reagent Kits v3.1. Barcoded, full-length cDNAs were then reverse-transcribed from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers which were used in Illumina bridge amplification. The Single Cell 5’ Protocol produced Illumina-ready sequencing libraries. A Single cell 5’ library comprised standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 5’ 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1, while Read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 were standard Illumina® sequencing primer sites used in paired-end sequencing. Library sequencing was performed on the Illumina HiseqTM 4000 by Gene Denovo Biotechnology Co., Ltd (Guangzhou, China).

value: hypothalamus

value: male

tag: age

value: 30 months


title: M1_P_16C5_D3

source_name: M1 macs, PBS and 16C5 antibody treatment

value: M1 macrophage


title: NAWM matched with the DSCL cases 1

type: RNA

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

country: United Kingdom

institute: The University of Sheffield

description: NAWM case

hyb_protocol: Approximately 5.5 μg amplified cDNA was fragmented, labelled and hybridised to Clariom S Array chips for 16 h at 45 °C in a rotating oven at 60 rpm.

scan_protocol: Using the Fluidics Station 400 and GeneChip Operating System, a series of washing steps followed to remove any unbound DNA, before each microarray was stained and scanned using the GeneChip 3000 scanner.

data_processing: Affymetrix Expression Console software (Affymetrix®, Stockport, UK) was employed to quality control the data and principal component analysis (PCA) in Qlucore Omics Explorer software (Qlucore, Lund, Sweden) was used to visually inspect the data and identify sample outliers. Transcriptome Analysis Console (TAC) software, version 4.1.1 (Affymetrix®, UK) was used to analyse and compare the gene expression profile of the 3 groups.

label: biotin

source_name: Human post-mortem tissue

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted from the LCM-isolated cells using the PicoPure RNA isolation kit (Life technologies: Applied Biosystems, USA).

tag: gender

tag: age (yrs)


title: CTRL_Female_3

tag: tissue


title: R413SCAbx

value: Brain

tag: strain

value: Sprague-Dawley (WT)

value: antibiotics + short-chain fatty acid


title: CTRL_Male_4


title: B1_AGY1612_Gen0_RepA

description:
GaschNuSeq_1002
Batch1_Dutcher_barcode_cts.csv

tag: genetic lineage

value: North American

value: plasmid DNA


title: B1_AGY1614_Gen0_RepA

description:
GaschNuSeq_1004
Batch1_Dutcher_barcode_cts.csv

tag: generation


title: R406SC

source_name: Rat, Nucleus Accumbens, short-chain fatty acids

value: Short-chain fatty acids


title: R412SCAbx


title: M0_P_16C5_D3

source_name: M0 macs, PBS and 16C5 antibody treatment

value: M0 macrophage

value: PBS

value: Donor 3

value: anti-ILT3 16C5


title: moDC_P_16C5_D3

source_name: MoDCs, PBS and 16C5 antibody treatment

value: Monocyte-derived DC


title: B1_AGY1611_Gen10_RepA

description:
GaschNuSeq_1005
Batch1_Dutcher_barcode_cts.csv

tag: media


title: CTRL_Male_1

value: Gastrocnemius Muscle

value: Male

value: untreated


title: M2c_F_KLH_D3

source_name: M2c macs, fibronectin and control antibodoy treatment

value: M2c macrophage

value: Fibronectin

value: anti-KLH (control)


title: CD11cloMinclelo, bio rep 3

city: Hachioji

first: Kenichi

last: Asano

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
Adaptor sequences were removed from raw data using Trimmomatic (ver. 0.39.0).
Sequencing reads after trimming were aligned to a mouse reference genome sequence (GRCm38/mm10) in the HISAT2 (ver. 2.2.1).
Read counts per gene were calculated using featureCounts (ver.2.0.1) based on GENCODE gene annotation version M25.
The transcripts per million (TPM) normalization was done according to the length of each gene and the sum of mapped reads.
Assembly: GRCm38/mm10

source_name: Liver macrophages

extract_protocol:
Total RNA from sorted cells was extracted with an RNeasy Micro Kit (QIAGEN).
cDNA was synthesized and amplified using an NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). RNA-seq libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs).

value: Liver macrophages

tag: genotype

value: WT

value: CDA-HFD


title: B1_AGY1611_Gen0_RepA

description:
GaschNuSeq_1001
Batch1_Dutcher_barcode_cts.csv

value: North American

tag: molecule type


title: R404SC

value: Brain

value: Sprague-Dawley (WT)


title: R403SC

value: Short-chain fatty acids


title: B1_AGY1612_Gen10_RepA

description:
GaschNuSeq_1006
Batch1_Dutcher_barcode_cts.csv

value: plasmid DNA


title: M2a_F_KLH_D3

source_name: M2a macs, fibronectin and control antibody treatment

tag: cell type

value: M2a macrophage

tag: plate coating

value: Donor 3


title: M1_F_KLH_D3

source_name: M1 macs, fibronectin and control antibody treatment

value: M1 macrophage

tag: donor

tag: antibody treatment


title: R402SC

tag: treatment


title: B1_AGY1613_Gen10_RepA

description:
GaschNuSeq_1007
Batch1_Dutcher_barcode_cts.csv


title: CD11cloMinclelo, bio rep 2


title: CTRL_Male_5

value: Gastrocnemius Muscle

tag: Sex

tag: treatment dose

value: drinking water


title: CTRL_Male_3

value: Male

value: untreated

tag: experimental batch


title: R407SC


title: B1_AGY1613_Gen0_RepA

description:
GaschNuSeq_1003
Batch1_Dutcher_barcode_cts.csv


title: tolDC_P_16C5_D3

source_name: TolDCs, PBS and 16C5 antibody treatment

value: Tolerogenic DC

value: PBS

value: anti-ILT3 16C5


title: set2 deletion, prp43-1 37 degrees

city: Los Angeles

first: Stephen

last: Douglass

address: 5128 TLSB Terasaki Life Sciences Building, 610 Charles Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
set2_prp43-1_37
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 prp43-1 set2Δ

data_processing:
Illumina CASAVA used for basecalling
Reads demultiplexed requiring exact barcode match
Paired-end reads merged
Unfiltered reads aligned using STAR v2.4.0 allowing 6 mismatches, no gaps
Unaligned reads aligned using STAR v2.4.0 allowing 0 mismatches, 1 gap
All reads aligned using STAR v2.4.0 allowing 2 mismatches, no gaps to both genome and junctions defined in previous step
Genome_build: sacCer3
Supplementary_files_format_and_content: The processed data file is read counts for novel splice sites in each sample

growth_protocol: Cells were grown to OD 0.3 in YPD at 25 degrees C.

extract_protocol:
RNA was extracted by hot phenol:chloroform:isoamyl alcohol extraction. 20 ug of total RNA was then treated with DNase I (Roche).
rRNA-depleted RNA
Library was constructed using TRUseq V2 kit (Illumina)

tag: temperature

value: 37 degrees

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 prp43-1 set2{delta}

tag: ploidy

value: Haploid


title: CTRL_Male_2

tag: tissue


title: tolDC_F_KLH_D3

source_name: TolDCs, fibronectin and control antibody treatment

value: Fibronectin

value: anti-KLH (control)


title: M0_F_KLH_D3

source_name: M0 macs, fibronectin and control antibody treatment

value: M0 macrophage


title: CD11cloMinclelo, bio rep 1

value: Liver macrophages

value: WT

value: CDA-HFD


title: R401SC

value: Brain

tag: strain

value: Sprague-Dawley (WT)

value: Short-chain fatty acids


title: CD11chiMinclehi, bio rep 3


title: set1 deletion, prp43-1 37 degrees

description:
set1_prp43-1_37
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 prp43-1 set1Δ

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 prp43-1 set1{delta}


title: set1 deletion, prp43-1 25 degrees

description:
set1_prp43-1_25
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 prp43-1 set1Δ

value: 25 degrees


title: R312Abx

source_name: Rat, Nucleus Accumbens, antibiotics (microbiome depletion)

value: Antibiotics


title: moDC_F_KLH_D3

source_name: MoDCs, fibronectin and control antibody treatment

value: Monocyte-derived DC

value: Donor 3


title: set2 deletion, prp43-1 25 degrees

description:
set2_prp43-1_25
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 prp43-1 set2Δ


title: CD11chiMinclehi, bio rep 2


title: CD11chiMinclehi, bio rep 1


title: prp43-1 37 degrees

description:
prp43-1_37
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 prp43-1

value: 37 degrees

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 prp43-1


title: R309Abx


title: M2c_P_KLH_D3

source_name: M2c macs, PBS and control antibody treatment

value: M2c macrophage

value: PBS


title: R209Abx


title: prp43-1 25 degrees

description:
prp43-1_25
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 prp43-1

value: Haploid


title: M2a_P_KLH_D3

source_name: M2a macs, PBS and control antibody treatment

value: M2a macrophage

value: anti-KLH (control)


title: R207Abx


title: set2 deletion 37 degrees

description:
set2_37
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 set2Δ

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 set2{delta}


title: R306H2O

source_name: Rat, Nucleus Accumbens, water control

value: H2O (control)


title: set2 deletion 25 degrees

description:
set2_25
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 set2Δ


title: D1 Con 5 Sirt1-KO

city: Phoenix

first: Hee-Dae

last: Kim

state: AZ

address: 425 N 5th St

department: Basic Medical Sciences

institute: University of Arizona College of Medicine

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC.
Reads were aligned using STAR.
Individual sample reads were quantified using HTseqand normalized via Relative Log Expression (RLE) using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Brain

growth_protocol: Mice were housed on a 12 hr light-dark cycle with access to food and water ad libitum.

extract_protocol:
Six NAc tissue punches (2 mm) from two RT; D1-Cre or RT; D2-Cre mice are homogenized in 1 ml of homogenization buffer (Sanz et al., 2009) for each sample (2 mice, pooled for each sample). Samples are then centrifuged at 4°C, 10,000 g for 10 min and 750 μl of clear supernatants are mixed with 5 μg of HA-antibody (Abcam, #ab9110), and incubated on a gentle rotator at 4°C overnight. Remaining supernatants are saved for input samples at -80°C until RNA purification. The next day, 200 μl of magnetic beads (Dynabeads anti-rabbit IgG; Life technology) are added and incubated overnight with constant rotation. The following day, magnetic beads are washed 3 times in the magnetic rack for 10 min with a high salt wash buffer. Each RNA sample was extracted using Direct-zol miniprep kit (Zymo Research) and subjected to RNA-seq. For quality control, RNA integrity (RIN) values were measured and samples with RIN < 7 were excluded.
Purified RNA samples from RiboTag immunoprecipitation (500 ng of RNA for each) were prepped for libraries after poly-A selection (KAPA Stranded mRNA-Seq Kit, Roche) and the libraries were sequenced in NextSeq500 (Illumina).

treatment_protocol: Test mice (RT; Sirt1-floxed; D1-Cre) were exposed to an unfamiliar and aggressive male CD1 retired breeder mouse for 10 min per day for up to 10 days. Following direct interaction with the CD1 aggressor, animals were placed in an adjacent compartment of the same cage for the next 24 hrs with sensory, but not physical contact. Control animals were housed in equivalent cages but with members of the same strain. 24 hrs following the last social defeat, animals were assayed on the social interaction test and sorted into either susceptible or unsusceptible (resilient) phenotypes based on interaction scores.

value: Male

value: Brain

tag: brain region

value: Nucleus accumbens (NAc)

value: RT; Sirt1-floxed; D1-Cre

value: Chronic social defeat stress (control:no social defeat)


title: M1_P_KLH_D3

source_name: M1 macs, PBS and control antibody treatment

value: M1 macrophage


title: D1 Con 3 Sirt1-KO


title: M0_P_KLH_D3

source_name: M0 macs, PBS and control antibody treatment

value: M0 macrophage


title: D1 Con 4 Sirt1-KO


title: R305H2O

value: Sprague-Dawley (WT)


title: tolDC_P_KLH_D3

source_name: TolDCs, PBS and control antibody treatment

value: Tolerogenic DC

value: Donor 3


title: set1 deletion 25 degrees

description:
set1_25
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 set1Δ

value: 25 degrees

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 set1{delta}


title: WT

city: Guangzhou

first: Yingying

last: Zhao

address: Kaiyuan Avenue

department: Chinese Academy of Sciences Guangzhou Branch

institute: Guangzhou Institutes of Biomedicine and Health

data_processing:
RNA-seq: Data quality control for raw data using FastQC (v0.11.4)
RNA-seq: Preprocessing of raw reads using cutadapt (version 2.6)
RNA-seq: Read aligned to the human reference genome using STAR (version 2.7.10a)
RNA-seq: Quantification of gene expression of RNA-seq using RSEM (v1.2.28)
scRNA-seq: Data quality control for raw data using FastQC (v0.11.4)
scRNA-seq: Read aligned to the human reference genome using STARsolo (version 2.7.10a)
scRNA-seq:The BAM files in the results of STARsolo were visualized using IGV(2.8.9)
Assembly: hg38
Supplementary files format and content: RNA-seq: tab-delimited table containing gene count values, TPM values, FPKM values
Supplementary files format and content: RNA-seq: tab-delimited table containing isoform count values, TPM values, FPKM values

source_name: midbrain

extract_protocol:
RNA-seq: To extract the total RNAs, organoids were collected and lysed with 1 ml TRIzol reagent (MRC, TR118-200), followed by adding 200 μL chloroform. After centrifugation (14,000 ×g for 10 min at 4°C), the total RNAs in the supernatant were precipitated with isopropanol. 1ug RNAs were subjected to RNA-seq library construction.
scRNA-seq: Brain organoids at D21 and D30 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153).
RNA-seq: RNA Sequencing libraries were prepared according to the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme).
scRNA-seq: 3'-library was constructed using Chromium Single Cell Reagent Kits v2 (10X GENOMICS).

value: midbrain

value: WT


title: KI

value: KI


title: R301H2O


title: R202H2O


title: M2c_F_16C5_D2

source_name: M2c macs, fibronectin and 16C5 antibodoy treatment

value: M2c macrophage

value: Fibronectin

value: Donor 2

value: anti-ILT3 16C5


title: D1 Con 1 Sirt1-KO

value: Male

value: Brain

value: Nucleus accumbens (NAc)


title: R201H2O

value: H2O (control)


title: Wildtype 37 degrees

description:
Wildtype_37
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: 37 degrees

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: Haploid


title: set1 deletion 37 degrees

description:
set1_37
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 set1Δ


title: Wildtype 25 degrees

description:
Wildtype_25
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: moDC_P_KLH_D3

source_name: MoDCs, PBS and control antibody treatment

value: Monocyte-derived DC

value: PBS

value: Donor 3

value: anti-KLH (control)


title: bladder_Tom_plus

city: Fukushima

first: Satoru

last: Meguro

state: Fukushima

institute: Fukushima Medical University

description: 10X Genomics

data_processing:
The Cell Ranger package (version 7.0.0) was utilized to process unique molecular identifiers (UMIs) and barcodes and align the transcripts to a mm10 mouse reference genome, which was supplied with tdTomato and WPRE sequences manually.
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: bladder

extract_protocol:
The bladder from a 25-month-old male p16-CreERT2-tdTomato mouse was harvested two weeks after consecutive five days i.p injection of tamoxifen. The harvested bladder tissue was minced using a blade and then subjected to agitation two times using 18 G and 21 G needles during one-hour incubation at 37℃ in 2ml PBS containing 5 mg Collagenase Type 4 (GIBCO) and 5 KU/ml of DNase I (Sigma-Aldrich). The cell suspension was filtered through a 70 µm strainer (Falcon), followed by centrifugation (800 x g, 4℃, 3 minutes). The pellet was then resuspended in a wash buffer (4% FBS in PBS). After pelleting the cells, they were resuspended in wash buffer containing 10% FcR blocking reagent (MACS) for 15 minutes. Subsequently, the cells were stained with an anti-CD45 antibody (Biolegend) for 30 minutes at 4°C in the absence of light. After pelleted, cells were resuspended in wash buffer containing with 0.1 µg/ml DAPI (Cell Signaling Technology) to exclude dead cells during sorting. The CD45-/DAPI-/Tomato+ and CD45-/DAPI-/Tomato- cells were sorted by using BD FACSAria SORP (BD Bioscience).
For the scRNA-seq library construction, we followed the manufacturer’s instructions of 10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1.

value: bladder

value: All


title: Postculture1_screen4_04

city: Brookings

first: Natalie

middle: W

last: Thiex

state: SD

address: 1390 College Ave

department: Biology & Microbiology

institute: South Dakota State University

data_processing:
Counts of sgRNA reads generated and mapped to Brie library sgRNAs using MAGeCK 0.5.9.2
We used a paired MAGeCK test so we could analyze data from four independent CRISPR screens
Assembly: Brie Library
Supplementary files format and content: Counts.csv file contains frequency per sgRNA in each CRISPR screen per condition
Supplementary files format and content: rra_paired.gene_summary.txt contains the MAGeCK RRA analysis output comparing input to post-culture sgRNA read frequencies from counts.csv

source_name: Bone-marrow

growth_protocol: Following bone-marrow cell isolation, cells were cultured in bone-marrow medium (BMM) containing Dulbecco’s Modified Eagle Medium (4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate), 20% heat-inactivated fetal bovine serum and 30% L-cell supernatant (a source of colony-stimulating factor-1), 10,000 IU penicillin and 10 mg/mL streptomycin, and 5.7 mM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was extracted from cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher) and the sgRNA library was amplified by a single-step PCR protocol (Broad Institute) for NGS using barcoded primers with staggered sequences. PCR product from multiple PCR reactions was pooled and gel purified and quantified by Qubit Fluorometer and subjected to sequencing on Illumina Nextseq 500 with 75 reads.
Mouse Brie CRISPR knockout pooled library developed by David Root and John Doench was obtained from Addgene (Addgene #73633) was amplified in Stable 3 competent E. coli (Thermofisher) and subjected to next-generation-sequencing (NGS) to determine the distribution of sgRNAs in the library. To produce Lentivirus, 1.8 x 106 NIH 293T cells were seeded in six 10-cm plates and transfected the following day with 6 μg sgRNA pooled library in lentiGuide-Puro (Addgene# 73633), 6 μg psPAX2 plasmid, 1 μg pVSVG plasmid, and 0.024 mg polyethyleneimine (PEI). After 48 h, the lentivirus was harvested, centrifuged, and aliquoted into multiple 15 mL tubes and stored at -80o C or - 150o C. The functional titer of the lentivirus was determined by live-cell counting after puromycin selection.
The parameters for how the library sequenced - chip: 75 high fidelity read

treatment_protocol: Primary Macrophages expressing Cas9 were transduced with the Brie Library plasmids (Input) packaged in lentivirus at low multiplicity of infection (MOI) (0.3) to achieve 50 fold representation of each sgRNA in the Brie Mouse library.  After 48 h, transduced cells were selected with 5 ug/ml puromycin for 2 days and cultured another 12-14 days (post-culture)

value: Bone-marrow

tag: cell line

value: Primary Macrophage

value: PCR amplicon from genomic DNA


title: M1_F_16C5_D2

source_name: M1 macs, fibronectin and 16C5 antibody treatment

value: M1 macrophage

value: Fibronectin

value: Donor 2

value: anti-ILT3 16C5


title: Postculture1_screen4_03


title: Naive OSKLH iPSC_6 (Methylation)

type: genomic

city: San Francisco

first: Akira

last: Kunitomi

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

description:
SAMPLE 32
Naive induced pluripotent stem cells derived from  adult periferal blood mononuclear cells

hyb_protocol: The bisulfite conversion of 500 ng genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research), and the bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K or EPIC BeadChip Kit using standard Illumina protocol

scan_protocol: Using illumina iScan according to recommended scanner setting

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates. Naive PSCs were cultured on iMEFs and maintained in t2iLGö+Y medium.

extract_protocol: Genomic DNA were extracted from cell lysates using the AllPrep DNA/RNA Mini Kit (QIAGEN)

value: Human induced pluripotent stem cells

tag: gender

value: Female


title: Naive OSKLH iPSC_4 (Methylation)

description:
SAMPLE 30
Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Postculture1_screen4_02

tag: genotype


title: Postculture1_screen4_01

tag: molecule type


title: Naive OSKLH iPSC_5 (Methylation)

description:
SAMPLE 31
Naive induced pluripotent stem cells derived from adult periferal blood mononuclear cells

tag: cell type


title: AEP-knockout cortex, irradiated, Day3, rep 3

city: Shanghai

first: Ouwen

last: Qiu

address: 160 Pujian Road

department: Brain Injury Center, Department of Neurosurgery

institute: Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
 Trimmomatic v 0.36
Remove adaptor sequence if reads contains.
Remove low quality bases from reads 3’ to 5’ (Q < 20)
Remove low quality bases from reads 5’ to 3’ (Q < 20)
Use a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp)
 Remove reads with reads length less than 35 nt and its pairing reads.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw conunts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: cortex

extract_protocol:
Total RNA was extracted using the Total RNA Extractor (Trizol) kit (B511311, Sangon, China) according to the manufacturer’s protocol, and treated with RNase-free DNase I to remove genomic DNA contamination. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: cortex

value: AEP knockout

value: whole brain irradiation


title: tolDC_F_16C5_D2

source_name: TolDCs, fibronectin and 16C5 antibody treatment

value: Tolerogenic DC

tag: plate coating


title: AEP-knockout cortex, irradiated, Day3, rep 2


title: Naive OSKLH iPSC_3 (Methylation)

description:
SAMPLE 29
Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Input_screen4_04


title: moDC_F_16C5_D2

source_name: MoDCs, fibronectin and 16C5 antibody treatment

value: Monocyte-derived DC

tag: donor


title: Naive OSKLH iPSC_2 (Methylation)

description:
SAMPLE 28
Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: AEP-knockout cortex, irradiated, Day3, rep 1


title: Input_screen4_03


title: M2c_P_16C5_D2

source_name: M2c macs, PBS and 16C5 antibody treatment

value: M2c macrophage

value: PBS

tag: antibody treatment


title: wildtype cortex,irradiated, Day 3, rep 3

value: WT

tag: treatment


title: Input_screen4_02

value: Bone-marrow


title: M2a_F_16C5_D2

source_name: M2a macs, fibronectin and 16C5 antibody treatment

value: M2a macrophage


title: Naive OSKLH iPSC_1 (Methylation)

description:
SAMPLE 27
Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: M2a_P_16C5_D2

source_name: M2a macs, PBS and 16C5 antibody treatment


title: Input_screen4_01

value: Primary Macrophage

value: PCR amplicon from genomic DNA


title: wildtype cortex,irradiated, Day 3, rep 2


title: Naive OSKL iPSC_5 (Methylation)

description:
SAMPLE 25
Naive induced pluripotent stem cells derived from adult periferal blood mononuclear cells


title: wildtype cortex,irradiated, Day 3, rep 1


title: Postculture1_screen3_04


title: bladder_Tom_minus

description: 10X Genomics

value: bladder

value: All


title: M1_P_16C5_D2

source_name: M1 macs, PBS and 16C5 antibody treatment

value: M1 macrophage

value: Donor 2

value: anti-ILT3 16C5


title: M0_F_16C5_D2

source_name: M0 macs, fibronectin and 16C5 antibody treatment

value: M0 macrophage

value: Fibronectin


title: Naive OSKL iPSC_6 (Methylation)

description:
SAMPLE 26
Naive induced pluripotent stem cells derived from  adult periferal blood mononuclear cells

value: Human induced pluripotent stem cells

value: Female


title: Postculture1_screen3_03


title: M0_P_16C5_D2

source_name: M0 macs, PBS and 16C5 antibody treatment


title: tolDC_P_16C5_D2

source_name: TolDCs, PBS and 16C5 antibody treatment

value: Tolerogenic DC


title: C1-4

city: Hohhot

first: Xin

address: No. 306, Zhaowuda Road, Saihan District, Hohhot, Inner Mongolia

institute: Inner Mongolia Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired_x0002_end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package   through one scaling normalized factor.Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=MNCJ01&display=history
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Helianthus annuus

source_name: root

extract_protocol:
The roots of the treated sunflower were quickly frozen in liquid nitrogen, and RNA was harvested using RNAprep Pure Plant Kit  (Polysaccharides&Polyphenolics-rich). NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) is used with total RNA to construct a sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

tag: age

value: 15 days after sowing

value: Virulent strain treatment(C)


title: C1-3


title: Naive OSKL iPSC_3 (Methylation)

description:
SAMPLE 23
Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Naive OSKL iPSC_4 (Methylation)

description:
SAMPLE 24
Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Postculture1_screen3_02

value: Bone-marrow


title: C1-2


title: Naive OSKL iPSC_2 (Methylation)

description:
SAMPLE 22
Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: moDC_P_16C5_D2

source_name: MoDCs, PBS and 16C5 antibody treatment

value: Monocyte-derived DC

value: PBS


title: M2c_F_KLH_D2

source_name: M2c macs, fibronectin and control antibodoy treatment

value: M2c macrophage

value: anti-KLH (control)


title: Postculture1_screen3_01

value: Primary Macrophage

value: PCR amplicon from genomic DNA


title: Naive OSKL iPSC_1 (Methylation)

description:
SAMPLE 21
Naive induced pluripotent stem cells derived from adult human dermal fibroblasts


title: B1-3

value: Attenuated strain treatment(B)


title: B1-4


title: Input_screen3_04


title: Naive H9 ESC (Methylation)

description:
SAMPLE 20
Naive embryonic stem cells which were reset from the primed to naive state

value: Human embryonic stem cells


title: B1-2


title: M1_F_KLH_D2

source_name: M1 macs, fibronectin and control antibody treatment

value: M1 macrophage

value: Donor 2


title: Input_screen3_02


title: 201B7 (Methylation)

description:
SAMPLE 19
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

value: Human induced pluripotent stem cells


title: M2a_F_KLH_D2

source_name: M2a macs, fibronectin and control antibody treatment

value: M2a macrophage

value: Fibronectin


title: Input_screen3_01

source_name: Bone-marrow


title: M0_F_KLH_D2

source_name: M0 macs, fibronectin and control antibody treatment

value: M0 macrophage


title: Input_screen3_03


title: KhES1 (Methylation)

description:
SAMPLE 18
Primed embryonic stem cells

source_name: Primed embryonic stem cells

value: Female


title: A2-2

value: root

value: 15 days after sowing

value: Wild-type, no treatment(A)


title: Postculture1_screen2_04

value: Bone-marrow


title: Primed H9 ESC (Methylation)

description:
SAMPLE 17
Primed embryonic stem cells


title: tolDC_F_KLH_D2

source_name: TolDCs, fibronectin and control antibody treatment

value: Tolerogenic DC


title: Primed OSKLH iPSC_8 (Methylation)

description:
SAMPLE 16
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: moDC_F_16C5_D3

source_name: MoDCs, fibronectin and 16C5 antibody treatment

value: Monocyte-derived DC

value: Donor 3

value: anti-ILT3 16C5


title: moDC_F_KLH_D2

source_name: MoDCs, fibronectin and control antibody treatment

value: anti-KLH (control)


title: Postculture1_screen2_03

value: Primary Macrophage

value: PCR amplicon from genomic DNA


title: M2c_P_KLH_D2

source_name: M2c macs, PBS and control antibody treatment

value: M2c macrophage

value: PBS

value: Donor 2


title: A2-1


title: M2a_P_KLH_D2

source_name: M2a macs, PBS and control antibody treatment

value: M2a macrophage


title: Primed OSKLH iPSC_7 (Methylation)

description:
SAMPLE 15
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

value: Human induced pluripotent stem cells


title: synovium, normal rep7

city: Kunming

first: Yang

last: Naixue

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: LPBR

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/cn/support/software/cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca fascicularis

source_name: synovium

extract_protocol:
Cartilage (~ 1 g) from intact and damaged regions of interest was minced finely with a sterile scalpel and collected in a 15 ml tube. A total of 15 ml of 0.4% Collagenase type II from Clostridium histolyticum (Sigma-Aldrich, Mo) made up in phosphate-bufered saline (PBS) and sterile filtered with a 0.22 μm filter, was added to the cartilage residua, incubated for 150 min at 37 °C rotating at 250 rpm. After enzymatic digestion, cells were pelleted by centrifugation, washed, sieved through a 30 μm cell strainer (Miltenyi Biotec, CA), pelleted by centrifugation again and resuspended in 1 ml PBS. Synovial membranes were dissected into small pieces, digested with 0.1% Collagenease Type IV from Clostridium histolyticum (Sigma-Aldrich, MO) in PBS for 1 h at 37 °C rotating at 250 rpm, then washed twice with PBS. Cells were centrifuged, washed, and sieved through a 30 μm cell strainer (Miltenyi Biotec, CA), pelleted by centrifugation again and resuspended in 1 ml PBS.
The GEMs(Gel Bead in Emulsion) were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined. The final library pool was sequenced on the Illumina Novaseq6000 instrument using 150-base-pair paired-end reads.

value: synovium

value: normal

tag: cell dose


title: Primed OSKLH iPSC_6 (Methylation)

description:
SAMPLE 14
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

value: Female


title: Postculture1_screen2_02


title: synovium, normal rep6


title: Postculture1_screen2_01


title: A2-3

value: root

value: 15 days after sowing

value: Wild-type, no treatment(A)


title: synovium, normal rep5


title: M1_P_KLH_D2

source_name: M1 macs, PBS and control antibody treatment

value: M1 macrophage


title: Primed OSKLH iPSC_4 (Methylation)

description:
SAMPLE 12
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Input_screen2_04

value: Bone-marrow


title: Primed OSKLH iPSC_5 (Methylation)

description:
SAMPLE 13
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: synovium, normal rep4


title: Input_screen2_03


title: synovium, normal rep3


title: tolDC_P_KLH_D2

source_name: TolDCs, PBS and control antibody treatment

value: Tolerogenic DC


title: R415SCAbx

source_name: Rat, Nucleus Accumbens, antibiotics (microbiome depletion) + short-chain fatty acids

value: Brain

value: Sprague-Dawley (WT)

value: antibiotics + short-chain fatty acid


title: Input_screen2_02

value: Primary Macrophage

value: PCR amplicon from genomic DNA


title: Primed OSKLH iPSC_3 (Methylation)

description:
SAMPLE 11
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: synovium, normal rep2


title: Primed OSKLH iPSC_2 (Methylation)

description:
SAMPLE 10
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: M2c_F_16C5_D1

source_name: M2c macs, fibronectin and 16C5 antibodoy treatment

value: M2c macrophage

value: Fibronectin

value: Donor 1

value: anti-ILT3 16C5


title: moDC_P_KLH_D2

source_name: MoDCs, PBS and control antibody treatment

value: Monocyte-derived DC

value: PBS

value: Donor 2

value: anti-KLH (control)


title: Input_screen2_01


title: Postculture1_screen1_04


title: synovium, normal rep1

value: synovium

value: normal


title: M2a_F_16C5_D1

source_name: M2a macs, fibronectin and 16C5 antibody treatment

value: M2a macrophage


title: M0_P_KLH_D2

source_name: M0 macs, PBS and control antibody treatment

value: M0 macrophage


title: Postculture1_screen1_03

value: Bone-marrow


title: Primed OSKLH iPSC_1 (Methylation)

description:
SAMPLE 9
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

value: Human induced pluripotent stem cells

value: Female


title: synovium, OA_model rep3

value: Osteoarthritis model


title: synovium, OA_model rep2


title: Postculture1_screen1_02

value: Primary Macrophage

value: PCR amplicon from genomic DNA


title: synovium, OA_model rep1


title: Postculture1_screen1_01


title: Primed OSKL iPSC_5 (Methylation)

description:
SAMPLE 5
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Primed OSKL iPSC_6 (Methylation)

description:
SAMPLE 6
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: moDC_F_16C5_D1

value: Fibronectin


title: Primed OSKL iPSC_4 (Methylation)

description:
SAMPLE 4
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: M0_F_16C5_D1

source_name: M0 macs, fibronectin and 16C5 antibody treatment

value: Donor 1


title: synovium, msc_treat rep5

value: Osteoarthritis model, msc treat


title: Primed OSKL iPSC_8 (Methylation)

description:
SAMPLE 8
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: M2c_P_16C5_D1

source_name: M2c macs, PBS and 16C5 antibody treatment

value: M2c macrophage

value: anti-ILT3 16C5


title: Primed OSKL iPSC_3 (Methylation)

description:
SAMPLE 3
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: synovium, msc_treat rep4


title: M1_F_16C5_D1

source_name: M1 macs, fibronectin and 16C5 antibody treatment

value: M1 macrophage


title: Input_screen1_02

source_name: Bone-marrow


title: M2a_P_16C5_D1

source_name: M2a macs, PBS and 16C5 antibody treatment

value: PBS


title: synovium, msc_treat rep3

value: synovium


title: synovium, msc_treat rep6


title: synovium, msc_treat rep2


title: M0_P_16C5_D1

source_name: M0 macs, PBS and 16C5 antibody treatment


title: tolDC_F_16C5_D1

source_name: TolDCs, fibronectin and 16C5 antibody treatment

value: Tolerogenic DC


title: tolDC_P_16C5_D1

source_name: TolDCs, PBS and 16C5 antibody treatment


title: Input_screen1_04


title: Primed OSKL iPSC_1 (Methylation)

description:
SAMPLE 1
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: cartilage, normal rep6

source_name: cartilage

value: cartilage

value: normal


title: AD+OB_7

city: DAEJEON

first: Jeeyoun

last: jung

address: Yuseong daero 1672

country: South Korea

institute: Korea institute of Oriental Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Skin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Skin

value: WT

value: AD+OB


title: AD+OB_5


title: M2c_F_KLH_D1

source_name: M2c macs, fibronectin and control antibodoy treatment

value: anti-KLH (control)


title: cartilage, normal rep7


title: AD+OB_6


title: synovium, msc_treat rep1

source_name: synovium


title: cartilage, normal rep4


title: AD+OB_4


title: Primed OSKL iPSC_2 (Methylation)

description:
SAMPLE 2
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

value: Human induced pluripotent stem cells

value: Female


title: moDC_P_16C5_D1

source_name: MoDCs, PBS and 16C5 antibody treatment

value: Monocyte-derived DC


title: AD+OB_2


title: cartilage, normal rep5


title: Input_screen1_01

value: Bone-marrow

value: Primary Macrophage

value: PCR amplicon from genomic DNA


title: M1_F_KLH_D1

source_name: M1 macs, fibronectin and control antibody treatment

value: Fibronectin

value: Donor 1


title: M1_P_16C5_D1

source_name: M1 macs, PBS and 16C5 antibody treatment

value: M1 macrophage

value: PBS

value: anti-ILT3 16C5


title: AD+OB_3


title: M2a_F_KLH_D1

source_name: M2a macs, fibronectin and control antibody treatment

value: M2a macrophage


title: cartilage, normal rep3

value: cartilage

value: normal


title: ovarian cancer cells knockdown with CHSY1 shRNA-2

city: Wuhan

first: Jinling

last: Huang

state: Hubei

address: Jiefang Road 238

department: Obstetrics & Gynecology,

institute: Renmin Hospital of Wuhan University

description: Gene expression data from human ovarian cancer cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip primeview human. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Cells were incubated at 37°C and 5% CO2

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: The shCHSY1 group cells were transfected with CHSY1 shRNA and the shCtrl cells were transfected with control shRNA

value: ovarian cancer


title: ovarian cancer cells knockdown with Control shRNA-2


title: ovarian cancer cells knockdown with Control shRNA-1


title: AD+OB_1

value: Skin

value: WT

value: AD+OB


title: ovarian cancer cells knockdown with Control shRNA-3


title: ovarian cancer cells knockdown with CHSY1 shRNA-1


title: cartilage, normal rep2


title: ovarian cancer cells knockdown with CHSY1 shRNA-3


title: AD_5

value: AD


title: AD_4


title: cartilage, OA_model rep3

value: Osteoarthritis model


title: cartilage, normal rep1


title: cartilage, OA_model rep1


title: cartilage, OA_model rep2


title: AD_3


title: AD_2


title: moDC_F_KLH_D1

source_name: MoDCs, fibronectin and control antibody treatment

value: Monocyte-derived DC

value: anti-KLH (control)


title: tolDC_F_KLH_D1

source_name: TolDCs, fibronectin and control antibody treatment

value: Tolerogenic DC


title: M0_F_KLH_D1

source_name: M0 macs, fibronectin and control antibody treatment

value: M0 macrophage

value: Fibronectin


title: AD_1


title: M2a_P_KLH_D1

source_name: M2a macs, PBS and control antibody treatment

value: Donor 1


title: Input_screen1_03

source_name: Bone-marrow

value: Bone-marrow

value: Primary Macrophage

value: PCR amplicon from genomic DNA


title: M1_P_KLH_D1

source_name: M1 macs, PBS and control antibody treatment

value: M1 macrophage

value: PBS


title: colon cancer cells, non-tumorigenic [EpCAM+, CD44neg, CD166neg], saline solution [mouse #3903]

city: Nutley

first: Piero

last: Dalerba

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation (CDI)

institute: Hackensack Meridian Health

description: colon cancer

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 7G and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing: Gene-expression values (fluorescent signal intensities) were normalized using the Robust Multi-chip Average (RMA) method with quantile normalization across all arrays, and then transformed to log2 values (Irizarry et al., Biostatistics, 4:249-264, 2003; Bolstad et al., Bioinformatics, 19:185-193, 2003).

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: Cancer cells were purified from solid tumors established by sub-cutaneus engraftment into adult, female, immune-deficient (NSG) mice (source: The Jackson Laboratory, stock #005557) of a human patient-derived xenograft (PDX) line derived from a moderately differentiated (G2) primary colon carcinoma (PDX-COLON-8).

extract_protocol: Sorted cells were centrifuged to form a pellet and flash-frozen in liquid nitrogen. Total RNA was extracted using the PureLink™ RNA Micro Scale Kit (Invitrogen).

treatment_protocol: Tumor-bearing animals were treated for 4 weeks by intra-peritoneal (i.p.) administration of either irinotecan (50 mg/g, once weekly) or saline solution (1 ml, once weekly). Solid tumors were then harvested and dissociated ino single-cell suspensions by mechanical mincing into small fragmnets, followed by enzymatic digestion with DNAse-I (100 units/ml) and collagenase-III (200 units/ml). Single-cell suspensions were stained first with monoclonal antibodies (anti-human-EpCAM-Alexa488, clone 9C4, BioLegend; anti-human-CD44-PE-Cy7, clone G44-26, BD Biosciences; anti-human-CD166/ALCAM-PE, clone 105902, R&D Systems; anti-mouse-H2-Kd-PacificBlue, clone SF1-1.1, BioLegend). Malignant cell populations corresponding to top-of-the-crypt (EpCAM+, CD44-, CD166-) and bottom-of-the-crypt (EpCAM+, CD44+, CD166+) phenotypes were isolated by FACS, after exclusion of dead cells (DAPI+), cell doublets (serial gating based on FSC-A vs. FSC-H and SSC-A vs. SSC-W profiles) and mouse cells (H2-Kd+), following previously published protocols (Dalerba et al., PNAS, 104:10158-10163, 2007; Dalerba et al., Nature Biotechnology, 29:1120-1127, 2011).

tag: tumor model

tag: mouse tag

tag: cell population

value: EpCAM+, CD44neg, CD166neg

value: saline solution


title: colon cancer cells, tumorigenic [EpCAM+, CD44+, CD166+], saline solution [mouse #3903]

description: colon cancer


title: cartilage, msc_treat rep4

tag: tissue

value: cartilage

value: Osteoarthritis model, msc treat


title: M0_P_KLH_D1

city: South San Francisco

first: Joshua

institute: NGM Biopharmaceuticals

data_processing:
Data raw reads were filtered using Trim Galore! to remove low quality and adaptor bases. Reads shorter than 20nt were discarded.
Filtered reads were mapped to UCSC hg19 genome sequences using STAR (v2.6.0a).
At last, counts of all samples were generated using featureCounts (v1.6.2), and edgeR (v3.22.3) was used to get normalized counts and perform differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression raw read counts in tabular data format

source_name: M0 macs, PBS and control antibody treatment

extract_protocol:
Cells were harvested in TRIzol and RNA was isolated by choroform extraction, follwed by purification with the Rneasy kit (Qiagen).
Total RNA was prepared for sequencing using the TailorMix Directional RNA Sample Preparation Kit (SeqMatic) and sequenced on an Illumina NovaSeq S1.


title: M2c_P_KLH_D1

source_name: M2c macs, PBS and control antibody treatment

value: M2c macrophage


title: colon cancer cells, tumorigenic [EpCAM+, CD44+, CD166+], saline solution [mouse #3731]

description: colon cancer


title: Lung, Kiss1r+/+;Kras

city: seoul

first: seoyeon

last: lee

state: State...

address: space21, preventive medicine, room 861

institute: KyungHee University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2.
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include read count values for each Sample.

source_name: lung

treatment_protocol: Each mice were given Ad5-CMV-cre via intratracheal infections at 6 weeks old.

value: lung

value: Kiss1r+/+; KrasG12D

value: Ad5-CMV-cre intratracheal infection


title: colon cancer cells, non-tumorigenic [EpCAM+, CD44neg, CD166neg], irinotecan [mouse #3735]

description: colon cancer

value: irinotecan (CPT-11)


title: colon cancer cells, non-tumorigenic [EpCAM+, CD44neg, CD166neg], saline solution [mouse #3731]

description: colon cancer


title: tolDC_P_KLH_D1

last: Lichtman

address: 333 Oyster Point Boulevard

source_name: TolDCs, PBS and control antibody treatment

value: Tolerogenic DC

value: anti-KLH (control)


title: Lung, Kiss1rflox/flox;Kras

value: Kiss1rf/f; KrasG12D


title: cartilage, msc_treat rep3

source_name: cartilage


title: cartilage, msc_treat rep2


title: moDC_P_KLH_D1

source_name: MoDCs, PBS and control antibody treatment

value: Monocyte-derived DC

value: Donor 1


title: Lung, Kiss1rflox/+;Kras

value: Kiss1rf/+; KrasG12D


title: cartilage, msc_treat rep1


title: colon cancer cells, non-tumorigenic [EpCAM+, CD44neg, CD166neg], irinotecan [mouse #3727]

description: colon cancer


title: FLAG-Ngn2 CUT&RUN on purified Ngn2 transduced Yy1+/+ astrocytes at 2 dpi from WT mice - rep1

status: Public on Apr 30 2024

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

library_source: genomic

data_processing:
*library strategy: CUT&RUN
Data was processed using the CUT-RUNTools-2.0 pipeline (PMID: 34244724).
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: primary mouse astrocytes

growth_protocol: transduced astrocytes at 2 dpi from WT and YY1 conditional knockout

extract_protocol:
The YY1, FLAG, cohesin (Rad21) and H3K27Ac CUT&RUN assays were performed as previously described with specific modifications (PMID: 28079019).
Briefly, 2-3.6 * 10^5 iNs were harvested, washed twice, and resuspended in wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete). Concavalin A beads (BioMag® Plus, Polyscience) were activated with bead activation buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Cells were incubated with 10 μl of activated beads for 10 minutes at room temperature. Following incubation, the beads were resuspended in a cold antibody buffer (2 mM EDTA in digitonin buffer) containing antibody (5 μg YY1 (D5D9Z) Rabbit mAb #46395, 2μg FLAG antibody (Sigma, #F3165-.2MG), 5μg Rad21 (Biozol, #GTX106012), 1 μg of H3k27Ac (Abcam #39133) and the mixture was incubated on a nutator overnight at 4°C.
On the next day, the beads were washed twice and resuspended in 0.75 μl of pAG-Mnase in digitonin buffer (0.1% digitonin, ThermoFisher Scientific, in wash buffer), and incubated for 10 minutes at room temperature on a rotator. Later, beads were washed twice with cold digitonin buffer and then resuspended in 50 μl of digitonin buffer containing 1 μl of 100 mM CaCl2. The suspension was incubated for 2 hours at 4°C on a nutator. Following the incubation, 33 μl of STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A (Thermo Fisher Scientific), 50 μg/mL Glycogen) was added to each reaction, and the mixture was incubated for 30 minutes at 37°C.
DNA extraction was performed using UltraPure Phenol:Chloroform:Isoamylalcohol (25:24:1, v/v, ThermoFisher Scientific) and precipitated with 100% ethanol, 1 μl of Glycogen, and 1/10th volume of 3M Sodium Acetate for 4-16 hours at -20°C. DNA was then dissolved in 10 μl of 1 mM Tris-HCl pH 8 and 0.1 mM EDTA.
CUT&RUN libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) using 6-30 ng of fragmented DNA. The quality of the CUT&RUN libraries was evaluated using the Agilent 2100 Bioanalyzer system (Agilent). Library was sequenced using 2x50bp reads.

treatment_protocol: CUT&RUN  protocol

value: primary mouse astrocytes


title: FLAG-Ngn2 CUT&RUN on purified Ngn2 transduced Yy1-/- astrocytes at 2 dpi - rep2


title: Yy1 CUT&RUN on purified GFP transduced astrocytes at 2 dpi- rep1

value: WT


title: FLAG-Ngn2 CUT&RUN on purified Ngn2 transduced Yy1+/+ astrocytes at 2 dpi from WT mice - rep2


title: Yy1 CUT&RUN on purified 9S-A phosphomutant form of Ngn2 Ngn2 transduced astrocytes at 2 dpi- rep1


title: Yy1 CUT&RUN on purified Ngn2 transduced astrocytes at 2 dpi- rep1


title: H3K27Ac CUT&RUN on purified 9S-A phosphomutant form of Ngn2 transduced astrocytes at 2dpi- rep1


title: H3K27Ac CUT&RUN on purified Ngn2 transduced astrocytes at 2dpi- rep1


title: colon cancer cells, tumorigenic [EpCAM+, CD44+, CD166+], irinotecan [mouse #3735]

description: colon cancer


title: Rad21 CUT&RUN on purified 9S-A phosphomutant form of Ngn2 transduced astrocytes at 2dpi- rep1


title: Rad21 CUT&RUN on purified Ngn2 transduced astrocytes at 2dpi- rep2


title: Rad21 CUT&RUN on purified GFP transduced astrocytes at 2dpi- rep2


title: Rad21 CUT&RUN on purified GFP transduced astrocytes at 2dpi- rep1


title: Rad21 CUT&RUN on purified Ngn2 transduced astrocytes at 2dpi- rep1


title: TAC1 D60 SNI IP 2

city: Montreal

first: Arkady

last: Khoutorsky

state: Quebec

address: 3655 Promenade Sir-William-Osler

country: Canada

institute: McGill University

description: GRP7__SC_TAC1_D60_SNI_IP_2_tpm, GRP7__SC_TAC1_D60_SNI_IP_2_tpm_percentile, GRP7__SC_TAC1_D60_SNI_IP_2_tpm_qn

data_processing:
RNA-seq read files (fastq files) were checked for quality by FastQC and read trimming was done based on the Phred score and per-base sequence content
Trimmed Reads were then mapped against the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR
Relative abundances in Transcripts Per Million (TPM) for every gene of every sample was quantified by stringtie
Assembly: Genome Reference Consortium Mouse Build 38 patch release 5
Supplementary files format and content: TAR packaging followed by a GNU zip (gzip), tab separated text files with columns for gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all coding genes [processed files tpms and degs SNI TRAP and RF.xlsx]
Library strategy: TRAP-seq

source_name: spinal cord

growth_protocol: Female C57BL/6 mice were purchased from Charles River Laboratories, Inc. (St. Constant, Quebec, Canada) at 6–7 weeks of age. On arrival at the in-house animal facility, the mice were placed in a group of 5 animals per cage with food and water ad libitum under a 12:12 h light/dark cycle (with the light period from 07:00-19:00 h) with ambient temperature (22 °C) and humidity maintained at 40%.

extract_protocol:
For TRAP immunoprecipitated (IP) samples were prepared by overnight incubation of cell lyate with with protein washed G-coated Dynabeads (Invitrogen) bound to 50 µg of anti-GFP antibodies (HtzGFP-19F7 and HtzGFP-19C8 antibodies). Subsequently, RNA was extracted from the IP and a fraction of the cell lysate (input) samples using Direct-zol RNA kit (Zymo Research). For Ribosome profiling, a fraction of cell clysate was reserved for mRNA-seq while the remaining was used to extract ribosome footprints (rFPs). rFPs were extracted by incubating the cell lysate with 5 µl of RNase I (Ambion, AM2295) per 250 µg of crude total RNA for 45 min at 4 °C and quenched by adding 20 µl of SUPERase-In (Ambion, AM2694) per 5µl of RNase I used followed by ultracentrifugation through a sucrose cushion at 71,000 rpm at 4 °C. Subsequently, RNA was extracted from both the crude cell lysate reserved for mRNA-seq and the resuspended rFP pellet using hot-phenol RNA extraction method with isopropanol based precipitation.
rRNA-depleted stranded (HMR)

treatment_protocol: Spared nerver injury or sham surgery was performed on mice and was followed by eithanization and dissection of tissue at day 4 for early time point and at day 60 or day 63 for late time point.

value: spinal cord

value: excitatory neurons


title: TAC1 D60 SHAM IP 3

description: GRP7__SC_TAC1_D60_SHM_IP_3_tpm, GRP7__SC_TAC1_D60_SHM_IP_3_tpm_percentile, GRP7__SC_TAC1_D60_SHM_IP_3_tpm_qn


title: Rad21 CUT&RUN on purified GFP transduced astrocytes at 2dpi- rep3


title: TAC1 D60 SNI IP 1

description: GRP7__SC_TAC1_D60_SNI_IP_1_tpm, GRP7__SC_TAC1_D60_SNI_IP_1_tpm_percentile, GRP7__SC_TAC1_D60_SNI_IP_1_tpm_qn


title: TAC1 D60 SHAM IP 2

description: GRP7__SC_TAC1_D60_SHM_IP_2_tpm, GRP7__SC_TAC1_D04_SHM_IP_2_tpm_percentile, GRP7__SC_TAC1_D04_SHM_IP_2_tpm_qn


title: TAC1 D60 SHAM IN 3

description: GRP7__SC_TAC1_D60_SHM_IN_3_tpm, GRP7__SC_TAC1_D60_SHM_IN_3_tpm_percentile, GRP7__SC_TAC1_D60_SHM_IN_3_tpm_qn


title: TAC1 D60 SNI IP 3

description: GRP7__SC_TAC1_D60_SNI_IP_3_tpm, GRP7__SC_TAC1_D04_SNI_IP_3_tpm_percentile, GRP7__SC_TAC1_D04_SNI_IP_3_tpm_qn


title: TAC1 D60 SNI IN 3

description: GRP7__SC_TAC1_D60_SNI_IN_3_tpm, GRP7__SC_TAC1_D60_SNI_IN_3_tpm_percentile, GRP7__SC_TAC1_D60_SNI_IN_3_tpm_qn


title: TAC1 D60 SHAM IN 2

description: GRP7__SC_TAC1_D60_SHM_IN_2_tpm, GRP7__SC_TAC1_D60_SHM_IN_2_tpm_percentile, GRP7__SC_TAC1_D60_SHM_IN_2_tpm_qn


title: TAC1 D60 SNI IN 2

description: GRP7__SC_TAC1_D60_SNI_IN_2_tpm, GRP7__SC_TAC1_D60_SNI_IN_2_tpm_percentile, GRP7__SC_TAC1_D60_SNI_IN_2_tpm_qn


title: FLAG-Ngn2 CUT&RUN on purified Ngn2 transduced Yy1-/- astrocytes at 2 dpi - rep1


title: TAC1 D60 SHAM IN 1

description: GRP7__SC_TAC1_D60_SHM_IN_1_tpm, GRP7__SC_TAC1_D60_SHM_IN_1_tpm_percentile, GRP7__SC_TAC1_D60_SHM_IN_1_tpm_qn


title: TAC1 D60 SHAM IP 1

description: GRP7__SC_TAC1_D60_SHM_IP_1_tpm, GRP7__SC_TAC1_D60_SHM_IP_1_tpm_percentile, GRP7__SC_TAC1_D60_SHM_IP_1_tpm_qn


title: TAC1 D60 SNI IN 1

description: GRP7__SC_TAC1_D60_SNI_IN_1_tpm, GRP7__SC_TAC1_D60_SNI_IN_1_tpm_percentile, GRP7__SC_TAC1_D60_SNI_IN_1_tpm_qn


title: TAC1 D4 SHAM IP 3

description: GRP5__SC_TAC1_D04_SHM_IP_3_tpm, GRP5__SC_TAC1_D04_SHM_IP_3_tpm_percentile, GRP5__SC_TAC1_D04_SHM_IP_3_tpm_qn


title: TAC1 D4 SHAM IP 2

description: GRP5__SC_TAC1_D04_SHM_IP_2_tpm, GRP5__SC_TAC1_D04_SHM_IP_2_tpm_percentile, GRP5__SC_TAC1_D04_SHM_IP_2_tpm_qn


title: TAC1 D4 SNI IP 3

description: GRP5__SC_TAC1_D04_SNI_IP_3_tpm, GRP5__SC_TAC1_D04_SNI_IP_3_tpm_percentile, GRP5__SC_TAC1_D04_SNI_IP_3_tpm_qn


title: colon cancer cells, tumorigenic [EpCAM+, CD44+, CD166+], irinotecan [mouse #3727]

description: colon cancer


title: TAC1 D4 SNI IP 2

description: GRP5__SC_TAC1_D04_SNI_IP_2_tpm, GRP5__SC_TAC1_D04_SNI_IP_2_tpm_percentile, GRP5__SC_TAC1_D04_SNI_IP_2_tpm_qn


title: TAC1 D4 SHAM IP 1

description: GRP5__SC_TAC1_D04_SHM_IP_1_tpm, GRP5__SC_TAC1_D04_SHM_IP_1_tpm_percentile, GRP5__SC_TAC1_D04_SHM_IP_1_tpm_qn


title: TAC1 D4 SHAM IN 3

description: GRP5__SC_TAC1_D04_SHM_IN_3_tpm, GRP5__SC_TAC1_D04_SHM_IN_3_tpm_percentile, GRP5__SC_TAC1_D04_SHM_IN_3_tpm_qn


title: TAC1 D4 SNI IP 1

description: GRP5__SC_TAC1_D04_SNI_IP_1_tpm, GRP5__SC_TAC1_D04_SNI_IP_1_tpm_percentile, GRP5__SC_TAC1_D04_SNI_IP_1_tpm_qn


title: TAC1 D4 SHAM IN 2

description: GRP5__SC_TAC1_D04_SHM_IN_2_tpm, GRP5__SC_TAC1_D04_SHM_IN_2_tpm_percentile, GRP5__SC_TAC1_D04_SHM_IN_2_tpm_qn


title: TAC1 D4 SNI IN 3

description: GRP5__SC_TAC1_D04_SNI_IN_3_tpm, GRP5__SC_TAC1_D04_SNI_IN_3_tpm_percentile, GRP5__SC_TAC1_D04_SNI_IN_3_tpm_qn


title: TAC1 D4 SNI IN 2

description: GRP5__SC_TAC1_D04_SNI_IN_2_tpm, GRP5__SC_TAC1_D04_SNI_IN_2_tpm_percentile, GRP5__SC_TAC1_D04_SNI_IN_2_tpm_qn


title: TAC1 D4 SHAM IN 1

description: GRP5__SC_TAC1_D04_SHM_IN_1_tpm, GRP5__SC_TAC1_D04_SHM_IN_1_tpm_percentile, GRP5__SC_TAC1_D04_SHM_IN_1_tpm_qn


title: TAC1 D4 SNI IN 1

description: GRP5__SC_TAC1_D04_SNI_IN_1_tpm, GRP5__SC_TAC1_D04_SNI_IN_1_tpm_percentile, GRP5__SC_TAC1_D04_SNI_IN_1_tpm_qn


title: GAD2 D60 SHAM IP 3

description: GRP6__SC_GAD2_D60_SHM_IP_3_tpm, GRP6__SC_GAD2_D60_SHM_IP_3_tpm_percentile, GRP6__SC_GAD2_D60_SHM_IP_3_tpm_qn

value: inhibitory neurons


title: GAD2 D60 SNI IP 3

description: GRP6__SC_GAD2_D60_SNI_IP_3_tpm, GRP6__SC_GAD2_D60_SNI_IP_3_tpm_percentile, GRP6__SC_GAD2_D60_SNI_IP_3_tpm_qn


title: GAD2 D60 SHAM IP 2

description: GRP6__SC_GAD2_D60_SHM_IP_2_tpm, GRP6__SC_GAD2_D60_SHM_IP_2_tpm_percentile, GRP6__SC_GAD2_D60_SHM_IP_2_tpm_qn


title: GAD2 D60 SNI IP 1

description: GRP6__SC_GAD2_D60_SNI_IP_1_tpm, GRP6__SC_GAD2_D60_SNI_IP_1_tpm_percentile, GRP6__SC_GAD2_D60_SNI_IP_1_tpm_qn


title: GAD2 D60 SHAM IN 3

description: GRP6__SC_GAD2_D60_SHM_IN_3_tpm, GRP6__SC_GAD2_D60_SHM_IN_3_tpm_percentile, GRP6__SC_GAD2_D60_SHM_IN_3_tpm_qn


title: GAD2 D60 SNI IP 2

description: GRP6__SC_GAD2_D60_SNI_IP_2_tpm, GRP6__SC_GAD2_D60_SNI_IP_2_tpm_percentile, GRP6__SC_GAD2_D60_SNI_IP_2_tpm_qn


title: GAD2 D60 SNI IN 3

description: GRP6__SC_GAD2_D60_SNI_IN_3_tpm, GRP6__SC_GAD2_D60_SNI_IN_3_tpm_percentile, GRP6__SC_GAD2_D60_SNI_IN_3_tpm_qn


title: GAD2 D60 SHAM IN 2

description: GRP6__SC_GAD2_D60_SHM_IN_2_tpm, GRP6__SC_GAD2_D60_SHM_IN_2_tpm_percentile, GRP6__SC_GAD2_D60_SHM_IN_2_tpm_qn


title: GAD2 D60 SHAM IN 1

description: GRP6__SC_GAD2_D60_SHM_IN_1_tpm, GRP6__SC_GAD2_D60_SHM_IN_1_tpm_percentile, GRP6__SC_GAD2_D60_SHM_IN_1_tpm_qn


title: GAD2 D60 SNI IN 2

description: GRP6__SC_GAD2_D60_SNI_IN_2_tpm, GRP6__SC_GAD2_D60_SNI_IN_2_tpm_percentile, GRP6__SC_GAD2_D60_SNI_IN_2_tpm_qn


title: GAD2 D4 SNI IP 3

description: GRP4__SC_GAD2_D04_SNI_IP_3_tpm, GRP4__SC_GAD2_D04_SNI_IP_3_tpm_percentile, GRP4__SC_GAD2_D04_SNI_IP_3_tpm_qn


title: GAD2 D4 SHAM IP 3

description: GRP4__SC_GAD2_D04_SHM_IP_3_tpm, GRP4__SC_GAD2_D04_SHM_IP_3_tpm_percentile, GRP4__SC_GAD2_D04_SHM_IP_3_tpm_qn


title: GAD2 D4 SHAM IP 2

description: GRP4__SC_GAD2_D04_SHM_IP_2_tpm, GRP4__SC_GAD2_D04_SHM_IP_2_tpm_percentile, GRP4__SC_GAD2_D04_SHM_IP_2_tpm_qn


title: GAD2 D4 SHAM IP 1

description: GRP4__SC_GAD2_D04_SHM_IP_1_tpm, GRP4__SC_GAD2_D04_SHM_IP_1_tpm_percentile, GRP4__SC_GAD2_D04_SHM_IP_1_tpm_qn


title: GAD2 D4 SHAM IN 1

description: GRP4__SC_GAD2_D04_SHM_IN_1_tpm, GRP4__SC_GAD2_D04_SHM_IN_1_tpm_percentile, GRP4__SC_GAD2_D04_SHM_IN_1_tpm_qn


title: GAD2 D4 SNI IP 1

description: GRP4__SC_GAD2_D04_SNI_IP_1_tpm, GRP4__SC_GAD2_D04_SNI_IP_1_tpm_percentile, GRP4__SC_GAD2_D04_SNI_IP_1_tpm_qn


title: GAD2 D4 SHAM IN 3

description: GRP4__SC_GAD2_D04_SHM_IN_3_tpm, GRP4__SC_GAD2_D04_SHM_IN_3_tpm_percentile, GRP4__SC_GAD2_D04_SHM_IN_3_tpm_qn


title: GAD2 D4 SNI IN 3

description: GRP4__SC_GAD2_D04_SNI_IN_3_tpm, GRP4__SC_GAD2_D04_SNI_IN_3_tpm_percentile, GRP4__SC_GAD2_D04_SNI_IN_3_tpm_qn


title: GAD2 D4 SHAM IN 2

description: GRP4__SC_GAD2_D04_SHM_IN_2_tpm, GRP4__SC_GAD2_D04_SHM_IN_2_tpm_percentile, GRP4__SC_GAD2_D04_SHM_IN_2_tpm_qn


title: GAD2 D4 SNI IN 1

description: GRP4__SC_GAD2_D04_SNI_IN_1_tpm, GRP4__SC_GAD2_D04_SNI_IN_1_tpm_percentile, GRP4__SC_GAD2_D04_SNI_IN_1_tpm_qn


title: GRP3__SC_D03_VEH_403_rFP

data_processing:
RNA-seq read files (fastq files) were checked for quality by FastQC and read trimming was done based on the Phred score and per-base sequence content
Trimmed Reads were then mapped against the reference genome and transcriptome (Gencode vM16 and GRCm38.p5) using STAR
Relative abundances in Transcripts Per Million (TPM) for every gene of every sample was quantified by stringtie
Assembly: Genome Reference Consortium Mouse Build 38 patch release 5
Supplementary files format and content: TAR packaging followed by a GNU zip (gzip), tab separated text files with columns for gene id (Gencode), gene name, locus, and TPMs for each RNA-seq and trap replicate for all coding genes [processed files tpms and degs SNI TRAP and RF.xlsx]
Library strategy: Ribo-seq

value: all cells


title: GRP3__SC_D03_VEH_404_mRNA


title: GAD2 D60 SHAM IP 1

description: GRP6__SC_GAD2_D60_SHM_IP_1_tpm, GRP6__SC_GAD2_D60_SHM_IP_1_tpm_percentile, GRP6__SC_GAD2_D60_SHM_IP_1_tpm_qn


title: GRP3__SC_D03_VEH_404_rFP


title: GRP3__SC_D03_VEH_403_mRNA


title: GRP3__SC_D03_CFA_304_mRNA


title: GRP3_DRG_D03_VEH_402_mRNA

source_name: dorsal root ganglia

value: dorsal root ganglia


title: GAD2 D60 SNI IN 1

description: GRP6__SC_GAD2_D60_SNI_IN_1_tpm, GRP6__SC_GAD2_D60_SNI_IN_1_tpm_percentile, GRP6__SC_GAD2_D60_SNI_IN_1_tpm_qn


title: GRP3__SC_D03_CFA_304_rFP


title: GRP3__SC_D03_CFA_303_mRNA


title: GRP3_DRG_D03_VEH_402_rFP


title: GRP3_DRG_D03_VEH_401_mRNA


title: GAD2 D4 SNI IP 2

description: GRP4__SC_GAD2_D04_SNI_IP_2_tpm, GRP4__SC_GAD2_D04_SNI_IP_2_tpm_percentile, GRP4__SC_GAD2_D04_SNI_IP_2_tpm_qn


title: GRP3_DRG_D03_CFA_305_rFP


title: GRP3_DRG_D03_CFA_305_mRNA


title: GRP3_DRG_D03_CFA_301_rFP


title: GAD2 D4 SNI IN 2

description: GRP4__SC_GAD2_D04_SNI_IN_2_tpm, GRP4__SC_GAD2_D04_SNI_IN_2_tpm_percentile, GRP4__SC_GAD2_D04_SNI_IN_2_tpm_qn


title: SC_D63_SNI_205_rFP


title: SC_D63_SNI_206_rFP


title: SC_D63_SNI_205_mRNA


title: SC_D63_SHM_208_rFP


title: SC_D63_SHM_208_mRNA


title: SC_D63_SHM_207_rFP


title: DRG_D63_SNI_106_rFP


title: Primed OSKL iPSC_7 (Methylation)

description:
SAMPLE 7
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

value: Human induced pluripotent stem cells

value: Female


title: GRP3__SC_D03_CFA_303_rFP


title: GRP3_DRG_D03_VEH_401_rFP


title: DRG_D63_SHM_108_mRNA


title: DRG_D63_SNI_106_mRNA


title: DRG_D63_SHM_108_rFP


title: DRG_D63_SHM_107_mRNA


title: DRG_D63_SNI_105_mRNA


title: SC_D04_SNI_202_rFP


title: GRP3_DRG_D03_CFA_301_mRNA


title: SC_D04_SNI_201_mRNA


title: SC_D04_SNI_201_rFP


title: SC_D63_SNI_206_mRNA


title: SC_D04_SHM_203_mRNA


title: SC_D04_SHM_204_mRNA


title: DRG_D63_SHM_107_rFP


title: DRG_D04_SNI_102_mRNA


title: DRG_D04_SHM_104_rFP


title: DRG_D04_SNI_101_mRNA


title: SC_D04_SHM_203_rFP


title: SC_D63_SHM_207_mRNA


title: DRG_D04_SHM_104_mRNA


title: SC_D04_SNI_202_mRNA


title: DRG_D04_SHM_103_mRNA


title: DRG_D04_SHM_103_rFP


title: SC_D04_SHM_204_rFP


title: A549 human lung carcinoma, RNaseL_KO, None, 3

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description:
AK136M
cdsrna_round_RNaseL_2.csv

data_processing:
Files from the same library run in multiple lanes on the sequencer were merged together.
Sequence reads were trimmed for adaptor sequence/low-quality sequence with bbduk.sh tool from bbtools software (v37.62).
Trimmed reads were mapped to a database of highly abundant human rRNA and tRNA sequences with bowtie2 (v 2.4.5)
Unmapped reads were then mapped to the human reference genome (GRCh38) with STAR (v2.7.10a), duplicated reads were removed with picard MarkDuplicates (v2.26.10)
Quantification of fragments per gene was carried out with the featureCounts tool from Subread software (v2.0.1) by counting reads falling within CDSs.
BigWig files were generated with bamCoverage tool from DeepTools (v3.5.1).
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file includes raw fragment counts per sample
Supplementary files format and content: bigWig

source_name: Lung

extract_protocol:
Total RNA was extracted from cell lysates using Direct-zol mini kit (Zymo) or Trizol reagent (Invitrogen) according to the manufacturer’s protocol.
Samples for sequencing were subject to rRNA depletion and library preparation by Illumina kits.

value: Lung

value: lung carcinoma

value: RNAseL KO


title: DRG_D04_SNI_102_rFP


title: A549 human lung carcinoma, RNaseL_KO, 25A, 3

description:
AK137M
cdsrna_round_RNaseL_2.csv


title: A549 human lung carcinoma, RNaseL_KO, polyIC, 3

description:
AK138M
cdsrna_round_RNaseL_2.csv

value: polyIC


title: A549 human lung carcinoma, WT, 25A, 5

description:
AK135M
cdsrna_round_RNaseL_2.csv


title: A549 human lung carcinoma, WT, polyIC, 4

description:
AK134M
cdsrna_round_RNaseL_2.csv


title: A549 human lung carcinoma, WT, polyIC, 3

description:
AK123M
cdsrna_round_RNaseL_2.csv


title: DRG_D04_SNI_101_rFP


title: A549 human lung carcinoma, WT, 25A, 4

description:
AK102M
cdsrna_round_RNaseL_2.csv


title: A549 human lung carcinoma, WT, None, 4

description:
AK117M
cdsrna_round_RNaseL_2.csv


title: A549 human lung carcinoma, WT, None, 3

description:
AK098M
cdsrna_round_RNaseL_2.csv


title: A549 human lung carcinoma, RNAseL KO, 0.25 µg/ml poly I:C, 4.5h

description:
AK138F
Ribo_count.csv

data_processing:
Samples were sequenced on Illumina HiSeq3000 or Novaseq. Reads are demultiplexed and trimmed but contain UMIs (Unique Molecular Identifier).
Reads were aligned to a library of human non-coding RNA genes (rRNAs and tRNAs) with bowtie 1 and those not matching were retained.
Samples had PCR duplicates removed. Then samples that were technical replicates (different libraries made from a biological sample) were merged and "F2" was included in the file name.
Reads were then aligned to hg38 human transcriptome with STAR. The aligned reads were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Wig files were created by STAR. All reads are 5' end aligned.
Assembly: hg38
Supplementary files format and content: Comma-delimited text file includes raw fragment counts per sample
Supplementary files format and content: Wig files
Library strategy: ribosome profiling

extract_protocol:
Ribosome profiling lysates were clarified, Rnase I treated, and separated over sucrose cushion. RNA was then extracted using trizol and footprints of the specified size were retained by gel purification.
Samples were prepared using the protocol published in McGlincy and Ingolia, 2017. Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. rRNA was subtracted using Ribo-Zero Illumina kit after ligation. cDNAs were then circularized and PCR amplified.

tag: fraction

value: 80S ribosome protected RNA (25-34 nt)


title: A549 human lung carcinoma, RNAseL KO, 1 µM 2-5A , 4.5h

description:
AK137F
Ribo_count.csv


title: A549 human lung carcinoma, RNAseL KO, Lipofectamine (Control), 4.5h

description:
AK136F
Ribo_count.csv

value: Control


title: A549 human lung carcinoma, WT, 0.25 µg/ml poly I:C, 4.5h, 2

description:
AK135F
Ribo_count.csv


title: A549 human lung carcinoma, WT, Lipofectamine (Control), 4.5h, 3

description:
AK133F
Ribo_count.csv


title: A549 human lung carcinoma, WT, Lipofectamine (Control), 4.5h, 2

description:
AK117F
Ribo_count.csv


title: A549 human lung carcinoma, WT, 0.25 µg/ml poly I:C, 4.5h, 1

description:
AK123F
Ribo_count.csv


title: A549 human lung carcinoma, RNaseL_KO, BSA electroporated, 4.5 h, 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence with bbduk.sh tool from bbtools software (v37.62).
Trimmed reads were mapped to a database of highly abundant human rRNA and tRNA sequences with bowtie2 (v 2.4.5)
Unmapped reads were then mapped to the human reference genome (GRCh38) with STAR (v2.7.10a), duplicated reads were removed with picard MarkDuplicates (v2.26.10)
Quantification of fragments per gene was carried out with the featureCounts tool from Subread software (v2.0.1) by counting reads falling within CDSs.
BigWig files were generated with bamCoverage tool from DeepTools (v3.5.1).
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file includes raw fragment counts per sample
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was extracted from cell lysates using Direct-zol mini kit (Zymo) or Trizol reagent (Invitrogen) according to the manufacturer’s protocol.
Samples for sequencing were subject to rRNA depletion and library preparation by Illumina Truseq kit.

value: BSA


title: A549 human lung carcinoma, RNaseL_KO, BSA electroporated, 4.5 h, 1


title: A549 human lung carcinoma, WT, 25A, 1


title: A549 human lung carcinoma, RNaseL_KO, Rnase A electroporated, 4.5 h, 2

value: RNase A


title: A549 human lung carcinoma, RNaseL_KO, Rnase A electroporated, 4.5 h, 1


title: A549 human lung carcinoma, RNaseL_KO, None, 2


title: A549 human lung carcinoma, WT, None, 5

description:
AK133M
cdsrna_round_RNaseL_2.csv


title: A549 human lung carcinoma, RNaseL_KO, None, 1


title: A549 human lung carcinoma, RNaseL_KO, 25A, 2


title: A549 human lung carcinoma, WT, 1 µM 2-5A , 4.5h, 1

description:
AK102F
Ribo_count.csv


title: A549 human lung carcinoma, WT, Lipofectamine (Control), 4.5h, 1

description:
AK098F
Ribo_count.csv


title: A549 human lung carcinoma, RNaseL_KO, BSA, 4.5h, rep2

data_processing:
*library strategy: ribosome profiling
Samples were sequenced on HiSeq3000. Reads are demultiplexed and trimmed but contain UMIs (Unique Molecular Identifier) and PCR duplicates. UMIs are  2 nt on the 5’ end and 5 nt on the 3’ end of the reads.
Reads were aligned to a library of human non-coding RNA genes (rRNAs and tRNAs) with bowtie 1 and those not matching were retained.
Samples had PCR duplicates removed.
Reads were then aligned to hg38 human transcriptome with STAR. The aligned reads were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Wig files were created by STAR.
Assembly: hg38
Supplementary files format and content: Comma-delimited text file includes raw fragment counts per sample
Supplementary files format and content: Wig files

extract_protocol:
Ribosome profiling lysates were clarified, Rnase I treated, and separated over sucrose cushion. RNA was then extracted using trizol and footprints of the specified size were retained by gel purification. Samples were prepared using the protocol published in McGlincy and Ingolia, 2017. Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. rRNA was subtracted using Ribo-Zero Illumina kit after ligation. cDNAs were then circularized and PCR amplified.
Samples for sequencing were subject to rRNA depletion and library preparation by Illumina Truseq kit.


title: A549 human lung carcinoma, RNaseL_KO, BSA, 4.5h, rep1


title: A549 human lung carcinoma, RNaseL_KO, 25A, 1


title: A549 human lung carcinoma, RNaseL_KO, Rnase A, 4.5h, rep1


title: A549 human lung carcinoma, WT, polyIC, 1


title: A549 human lung carcinoma, RNaseL_KO, Rnase A, 4.5h, rep2


title: A549 human lung carcinoma, WT, polyIC, 2


title: A549 human lung carcinoma, WT, None, 1


title: A549 human lung carcinoma, WT, 25A, 3


title: A549 human lung carcinoma, WT, 1 µM 2-5A , 4.5h, 2

description:
AK134F
Ribo_count.csv


title: A549 human lung carcinoma, RNaseL_KO, polyIC, 2


title: A549 human lung carcinoma, WT, None, 2


title: A549 human lung carcinoma, WT, 25A, 2


title: RNA-seq YCC10

status: Public on Apr 29 2024

city: Baltimore

first: Michael

middle: A

last: Beer

address: 733 N. Broadway

department: Biomedical Engineering and Genetic Medicine

institute: Johns Hopkins University

data_processing:
RNA-seq reads were aligned to the human genome (hg38) using TopHat2
Transcript abundances at the gene level were estimated by cufflinks
Gene expression from primary samples showing variation greater than zero were corrected for potential batch effects using ComBat
Assembly: hg38
Supplementary files format and content: RNA_table.tsv: gene name and log2 FPKM

extract_protocol:
Total RNA was extracted from 13 gastric cell-lines using RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.
Two micrograms of total RNA was used to create libraries with Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, California, USA) according to manufacturer’s instructions.

value: Gastric cancer cell line


title: A549 human lung carcinoma, RNaseL_KO, polyIC, 1


title: RNA-seq GSU

source_name: GSU

value: GSU


title: RNA-seq NCC20


title: RNA-seq AGS

source_name: AGS

value: AGS


title: RNA-seq YCC2


title: RNA-seq YCC6


title: RNA-seq NCC_STC_K140


title: RNA-seq NUGC3


title: RNA-seq LMSU

source_name: LMSU

value: LMSU


title: RNA-seq SH-10-TC


title: RNA-seq HS746T


title: RNA-seq GES1


title: Kidney, DbpA_KO_3

status: Public on Apr 26 2024

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
Before alignment to reference genome (mm10) each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using fastq-mcf. Reads shorter than 15 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/)) with default settings.
Assembly: mm10
Supplementary files format and content: Raw counts generated by Rsubread (Excel xlsx file)

source_name: Kidney

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Quiagen), 1.3 µg of total RNA was used for the construction of sequencing libaries.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). The RNA sequencing library was generated from 200ng total RNA using Ribo-off ( Vazyme) for mRNA purification followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) according to manufacture´s protocols. The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run) with an average of 5 x107 reads per RNA sample.

value: Kidney

value: Ybx3 knockout

value: control


title: Kidney, DbpA_KO_plus_IR_1

value: plus IRI


title: Kidney, DbpA_KO_plus_IR_3


title: Kidney, DbpA_KO_plus_IR_2


title: spatial transcriptomics of patient 1

status: Public on Apr 28 2024

first: guangyong

last: zheng

address: cailun road 1200

institute: shutcm

description: fresh frozen spatial transcriptome sequencing

data_processing:
raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate fastq files
sequences were aligned to GRCh 38 genome for gene experssion counting using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh 38
Supplementary files format and content: p1.barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: p1.features.tsv.gz list of gene IDs
Supplementary files format and content: p1.matrix.mtx.gz gene expression count data in matrix market exchange format
Supplementary files format and content: p1.aligned_fiducials.jpg aligned fiducials of the tissue image
Supplementary files format and content: p1.detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: p1.scalefactors_json.json scalefactors in json format
Supplementary files format and content: p1.tissue_hires_images.png hi-res image of tissue
Supplementary files format and content: p1.tissue_lowres_image.png low-res image of tissue
Supplementary files format and content: p1.tissue_position_list.csv list of spatial barcodes and the coordinates sepecifying spots
Library strategy: Spatial Transcriptomics

source_name: colon

extract_protocol:
fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expresssion Slides & Reagent kit according to manufacture's instruction
spatial transcriptomics

value: colon

tag: patient diagnosis

value: mucinous colorectal adenocarinoma

tag: disease state

value: tumor + normal


title: Kidney, DbpA_KO_2


title: Kidney, DbpA_KO_1


title: Kidney, DbpA_WT_plus_IR_2

value: Wildtype


title: Kidney, DbpA_WT_3


title: Kidney, DbpA_WT_plus_IR_3


title: Kidney, DbpA_WT_plus_IR_1


title: Kidney, DbpA_WT_2


title: DRG_D63_SNI_105_rFP

value: dorsal root ganglia

value: all cells


title: Co2888-gr rep2

status: Public on Apr 25 2024

city: Göttingen

first: Ting

last: Sun

state: Germany (DEU)

address: Hermann-Rein-Straße 3

department: Neurogenetics

institute: Max Planck Institute for Multidisciplinary Sciencesi

data_processing:
Data were demultiplexed using bcl2fastq and further controlled for sequencing quality using FastQC (Galaxy Version 0.72).
After verifying data quality, alignment was performed against reference genome Mmul10. Raw count profiles were extracted from aligned bam files using featureCounts, and normalized TPM values were calculated.
Assembly: Mmul_10
Supplementary files format and content: comma-delimited matrix include raw counts for RNA-seq results from both replicates
Supplementary files format and content: comma-delimited matrix include TPM normalized counts for RNA-seq results from both replicates

organism: Macaca mulatta

source_name: Cortex

growth_protocol: Tissue samples for trigeminal ganglia, brain cortex and hippocampus were obtained from two male animals sacrificed at age of 6 (animal 2817) and 7 (animal 2880) years for reasons unrelated to this project. Tissue samples were chopped into small (1 mm) pieces, transferred to separate Eppendorf tubes und incubated in 1 mL PBS containing 5 mg Collagenase IV. Samples were incubated for 1-3 hours at 37°C and 800 rpm in a thermomixer. After centrifugation for 5 min at 300 x g, cells were resuspended in medium and seeded separately into 6-well plates in a total volume of 3 mL/well. For neuronal tissue derived cells, DMEM/F12 was used as medium. All media were supplemented with 10% FCS and penicillin, streptomycin, gentamycin, nystatin and amphotericin B.

extract_protocol:
For RNA-isolation, selected MamuCo2888-gr and MamuCo2880-IT cells were seeded in 12-well plates in duplicate samples. After 24 h, total cellular RNA was extracted using the TRIZOL reagent (Ambion, Austin, TX, USA) following the manufacturer’s instructions.
Extracted total RNA was subjected to 50 bp single-end (for gr cell line) abd 50bp pair-end (for IT cell line) bulk RNA sequencing (Illumina HiSeq 4000).
50bp single-end (gr cell) and pair-end (IT cell) bulk RNA-seq

treatment_protocol: After few passages, cells were transduced with lentiviruses expressing human TERT, SV40 large T, or a mixture of genes shown to immortalize cells. To avoid TRIM5α-mediated restriction of HIV-based vectors we used a modified lentiviral system, which included a chimeric SIV/HIV-Gag protein. For the sequencing protocol, cells underwent selection with puromycin or hygromycin resistant after transduction with a gene mixture (termed “gr”).

value: Cortex

value: 6-7 years

value: WT

tag: Sex

value: male

tag: developmental stage

value: Adult


title: RNA-seq CLS145

tag: cell line

value: Gastric cancer cell line

tag: genotype


title: Co2888-gr rep1


title: PS3

status: Public on Apr 19 2024

city: Chongqing

first: Hang

address: No. 2 Tiansheng Road

institute: Southwest University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 50 raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about 50 clean reads  for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome  using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Brain

value: All cells in the brain tissue

tag: cell type

value: All cell types in brain tissue

value: Polystyrene nanoplastic intranasal exposure, 28 days


title: Kidney, DbpA_WT_1

value: Kidney

value: control


title: PS2


title: PS1


title: Control3

value: Sterile distilled water intranasal exposure, 28 days


title: Control2


title: L_Mnc1

status: Public on Apr 16 2024

first: He

last: Fei

address: 801 Heqing Road

department: Department of Obstetrics and Gynecology

institute: Shanghai Fifth People’s Hospital

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HLECs

growth_protocol: hLEC treated for 24h with conditioned media of Cervical Cancer cells with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Cervical cancer cells were cultured in DMEM supplemented with 10% of FBS until they reach 80% of confluence.Medium was then changed to ECM without FBS for 36 hours. This medium was collected, centrifuged for 5 minutesat 1500 rpm and filtered throught a 0.45mm pore membrane before use.The conditioned medium was prepared from the collected medium and the normal medium (ECM medium +5%FBS+1% ECGs+1% P/S double antibody) in a ratio of 6:4.

value: HLECs

value: Primary Human Lymphatic Endothilial cells (hLECs)

value: MDK NC

value: hLEC cells was used at 60%-70 confluency.  The media was substituted by 36h conditioned media from MS751 NC.  Cells were left to grow for 24h before being collected and processed for RNA-seq anlysis.


title: L_Mnc2